Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i5i-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.446 3.600 Wilson plot Bfac: 78.40 6266 reflections ( 99.19 % complete ) and 0 restraints for refining 4688 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3362 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2645 (Rfree = 0.000) for 4688 atoms. Found 17 (30 requested) and removed 34 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 4709 seeds are put forward NCS extension: 0 residues added, 4709 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.227 Round 2: 162 peptides, 33 chains. Longest chain 8 peptides. Score 0.274 Round 3: 182 peptides, 37 chains. Longest chain 9 peptides. Score 0.284 Round 4: 207 peptides, 39 chains. Longest chain 10 peptides. Score 0.336 Round 5: 214 peptides, 38 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 5 Chains 38, Residues 176, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 9020 restraints for refining 3814 atoms. 8333 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2331 (Rfree = 0.000) for 3814 atoms. Found 20 (24 requested) and removed 25 (12 requested) atoms. Cycle 2: After refmac, R = 0.2428 (Rfree = 0.000) for 3770 atoms. Found 18 (24 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2113 (Rfree = 0.000) for 3741 atoms. Found 8 (24 requested) and removed 22 (12 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1992 (Rfree = 0.000) for 3710 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.1894 (Rfree = 0.000) for 3684 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3769 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 9 peptides. Score 0.274 Round 2: 222 peptides, 40 chains. Longest chain 10 peptides. Score 0.368 Round 3: 234 peptides, 43 chains. Longest chain 9 peptides. Score 0.366 Round 4: 256 peptides, 47 chains. Longest chain 10 peptides. Score 0.380 Round 5: 236 peptides, 43 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 4 Chains 47, Residues 209, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8220 restraints for refining 3695 atoms. 7378 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2043 (Rfree = 0.000) for 3695 atoms. Found 22 (23 requested) and removed 35 (11 requested) atoms. Cycle 7: After refmac, R = 0.1969 (Rfree = 0.000) for 3653 atoms. Found 11 (23 requested) and removed 17 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1826 (Rfree = 0.000) for 3638 atoms. Found 4 (23 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.1873 (Rfree = 0.000) for 3617 atoms. Found 1 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.1778 (Rfree = 0.000) for 3600 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3690 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 9 peptides. Score 0.290 Round 2: 245 peptides, 45 chains. Longest chain 13 peptides. Score 0.373 Round 3: 234 peptides, 43 chains. Longest chain 11 peptides. Score 0.366 Round 4: 256 peptides, 44 chains. Longest chain 12 peptides. Score 0.417 Round 5: 251 peptides, 39 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 5 Chains 39, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8560 restraints for refining 3782 atoms. 7751 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1826 (Rfree = 0.000) for 3782 atoms. Found 21 (24 requested) and removed 31 (12 requested) atoms. Cycle 12: After refmac, R = 0.1677 (Rfree = 0.000) for 3754 atoms. Found 9 (24 requested) and removed 20 (12 requested) atoms. Cycle 13: After refmac, R = 0.1598 (Rfree = 0.000) for 3733 atoms. Found 7 (23 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.1564 (Rfree = 0.000) for 3722 atoms. Found 6 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.1465 (Rfree = 0.000) for 3704 atoms. Found 3 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 3782 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3797 seeds are put forward Round 1: 207 peptides, 45 chains. Longest chain 7 peptides. Score 0.257 Round 2: 243 peptides, 41 chains. Longest chain 15 peptides. Score 0.416 Round 3: 234 peptides, 40 chains. Longest chain 12 peptides. Score 0.403 Round 4: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.427 Round 5: 242 peptides, 39 chains. Longest chain 21 peptides. Score 0.438 Taking the results from Round 5 Chains 39, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8628 restraints for refining 3815 atoms. 7855 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1737 (Rfree = 0.000) for 3815 atoms. Found 17 (24 requested) and removed 22 (12 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1684 (Rfree = 0.000) for 3794 atoms. Found 8 (24 requested) and removed 22 (12 requested) atoms. Cycle 18: After refmac, R = 0.1633 (Rfree = 0.000) for 3764 atoms. Found 13 (24 requested) and removed 28 (12 requested) atoms. Cycle 19: After refmac, R = 0.1631 (Rfree = 0.000) for 3737 atoms. Found 9 (24 requested) and removed 19 (12 requested) atoms. Cycle 20: After refmac, R = 0.1598 (Rfree = 0.000) for 3724 atoms. Found 15 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3807 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3833 seeds are put forward Round 1: 198 peptides, 41 chains. Longest chain 11 peptides. Score 0.282 Round 2: 221 peptides, 41 chains. Longest chain 11 peptides. Score 0.353 Round 3: 211 peptides, 39 chains. Longest chain 12 peptides. Score 0.348 Round 4: 209 peptides, 33 chains. Longest chain 13 peptides. Score 0.419 Round 5: 222 peptides, 36 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 4 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8884 restraints for refining 3815 atoms. 8213 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1757 (Rfree = 0.000) for 3815 atoms. Found 22 (24 requested) and removed 24 (12 requested) atoms. Cycle 22: After refmac, R = 0.1659 (Rfree = 0.000) for 3794 atoms. Found 22 (24 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.1627 (Rfree = 0.000) for 3791 atoms. Found 15 (24 requested) and removed 18 (12 requested) atoms. Cycle 24: After refmac, R = 0.1497 (Rfree = 0.000) for 3783 atoms. Found 12 (24 requested) and removed 18 (12 requested) atoms. Cycle 25: After refmac, R = 0.1513 (Rfree = 0.000) for 3772 atoms. Found 14 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3855 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3869 seeds are put forward Round 1: 211 peptides, 43 chains. Longest chain 10 peptides. Score 0.296 Round 2: 222 peptides, 38 chains. Longest chain 14 peptides. Score 0.394 Round 3: 213 peptides, 38 chains. Longest chain 12 peptides. Score 0.367 Round 4: 221 peptides, 35 chains. Longest chain 17 peptides. Score 0.428 Round 5: 210 peptides, 37 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 4 Chains 35, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8725 restraints for refining 3815 atoms. 8016 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1521 (Rfree = 0.000) for 3815 atoms. Found 18 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.1545 (Rfree = 0.000) for 3800 atoms. Found 17 (24 requested) and removed 14 (12 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1402 (Rfree = 0.000) for 3791 atoms. Found 22 (24 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.1394 (Rfree = 0.000) for 3792 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1367 (Rfree = 0.000) for 3780 atoms. Found 20 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3860 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3879 seeds are put forward Round 1: 178 peptides, 39 chains. Longest chain 8 peptides. Score 0.243 Round 2: 190 peptides, 37 chains. Longest chain 8 peptides. Score 0.310 Round 3: 217 peptides, 40 chains. Longest chain 12 peptides. Score 0.353 Round 4: 225 peptides, 41 chains. Longest chain 12 peptides. Score 0.365 Round 5: 220 peptides, 40 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 4 Chains 42, Residues 184, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8595 restraints for refining 3813 atoms. 7855 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1666 (Rfree = 0.000) for 3813 atoms. Found 14 (24 requested) and removed 18 (12 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1617 (Rfree = 0.000) for 3789 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1696 (Rfree = 0.000) for 3781 atoms. Found 18 (24 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.1651 (Rfree = 0.000) for 3778 atoms. Found 19 (24 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.1621 (Rfree = 0.000) for 3775 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3842 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3855 seeds are put forward Round 1: 161 peptides, 36 chains. Longest chain 8 peptides. Score 0.228 Round 2: 165 peptides, 30 chains. Longest chain 11 peptides. Score 0.326 Round 3: 177 peptides, 31 chains. Longest chain 15 peptides. Score 0.350 Round 4: 167 peptides, 30 chains. Longest chain 11 peptides. Score 0.332 Round 5: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Chains 31, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6266 reflections ( 99.19 % complete ) and 8930 restraints for refining 3815 atoms. 8377 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1595 (Rfree = 0.000) for 3815 atoms. Found 16 (24 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.1618 (Rfree = 0.000) for 3810 atoms. Found 14 (24 requested) and removed 19 (12 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1507 (Rfree = 0.000) for 3800 atoms. Found 18 (24 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.1543 (Rfree = 0.000) for 3804 atoms. Found 18 (24 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1506 (Rfree = 0.000) for 3804 atoms. Found 21 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3880 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3901 seeds are put forward Round 1: 174 peptides, 36 chains. Longest chain 9 peptides. Score 0.272 Round 2: 179 peptides, 33 chains. Longest chain 14 peptides. Score 0.329 Round 3: 178 peptides, 32 chains. Longest chain 13 peptides. Score 0.339 Round 4: 174 peptides, 31 chains. Longest chain 15 peptides. Score 0.341 Round 5: 172 peptides, 33 chains. Longest chain 11 peptides. Score 0.307 Taking the results from Round 4 Chains 32, Residues 143, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8919 restraints for refining 3815 atoms. 8340 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1561 (Rfree = 0.000) for 3815 atoms. Found 23 (24 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.1580 (Rfree = 0.000) for 3817 atoms. Found 23 (24 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1619 (Rfree = 0.000) for 3824 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1598 (Rfree = 0.000) for 3822 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 45: After refmac, R = 0.1269 (Rfree = 0.000) for 3827 atoms. Found 8 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 3874 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3883 seeds are put forward Round 1: 127 peptides, 30 chains. Longest chain 5 peptides. Score 0.194 Round 2: 135 peptides, 26 chains. Longest chain 15 peptides. Score 0.284 Round 3: 139 peptides, 25 chains. Longest chain 15 peptides. Score 0.312 Round 4: 147 peptides, 22 chains. Longest chain 21 peptides. Score 0.381 Round 5: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.304 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6266 reflections ( 99.19 % complete ) and 8953 restraints for refining 3814 atoms. 8475 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1587 (Rfree = 0.000) for 3814 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1363 (Rfree = 0.000) for 3801 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1386 (Rfree = 0.000) for 3782 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1647 (Rfree = 0.000) for 3770 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:32:46 GMT 2018 Job finished. TimeTaking 64.82